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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ), 'gf_id' => 'HOM05D001225', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001225' ), 'data_identifier' => 'HOM05D001225', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001225', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '506', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p30520' => 'bna', 'A02p31640' => 'bna', 'A06p44700' => 'bna', 'A07p38640' => 'bna', 'Aa31LG2G8810' => 'aar', 'Aa31LG2G9160' => 'aar', 'Aa31LG4G2810' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.293' => 'aag', 'Actinidia11414' => 'ach', 'Actinidia11505' => 'ach', 'Actinidia13644' => 'ach', 'Actinidia21800' => 'ach', 'Actinidia24718' => 'ach', 'Actinidia26016' => 'ach', 'Actinidia28571' => 'ach', 'Actinidia31167' => 'ach', 'Actinidia31630' => 'ach', 'Actinidia32200' => 'ach', 'Actinidia39054' => 'ach', 'Ah.02g120400' => 'amhyb', 'Ah.10g024920' => 'amhyb', 'Ah.15g089980' => 'amhyb', 'Ah.15g095200' => 'amhyb', 'Ah.15g100600' => 'amhyb', 'AL2G14520' => 'aly', 'AL2G32170' => 'aly', 'AL5G10020' => 'aly', 'Aqoxy1G01257' => 'aox', 'Aqoxy5G02412' => 'aox', 'Aqoxy7G04088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4TG6YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8FJM7R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6H680' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GN14J4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7Z1X1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I83RFG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFL8P1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T94AR1' => 'arhy', 'AT1G10980' => 'ath', 'AT1G61670' => 'ath', 'AT1G72480' => 'ath', 'AT2G01070' => 'ath', 'ATR0006G037' => 'atr', 'ATR0684G149' => 'atr', 'ATR1127G089' => 'atr', 'ATR1127G110' => 'atr', 'ATR1127G119' => 'atr', 'Atru.chr1.4068' => 'acertr', 'Atru.chr12.205' => 'acertr', 'Atru.chr2.1213' => 'acertr', 'Atru.chr6.1088' => 'acertr', 'Atru.chr6.1101' => 'acertr', 'Atru.chr8.106' => 'acertr', 'AUR62001449' => 'cqu', 'AUR62003499' => 'cqu', 'AUR62006423' => 'cqu', 'AUR62009916' => 'cqu', 'AUR62017812' => 'cqu', 'AUR62029772' => 'cqu', 'BcaB02g07373' => 'bca', 'BcaB03g14997' => 'bca', 'BcaB03g15670' => 'bca', 'BcaB04g20356' => 'bca', 'BcaC06g31335' => 'bca', 'BcaC06g34221' => 'bca', 'BcaC08g45706' => 'bca', 'BcaC08g46697' => 'bca', 'BcaC08g46698' => 'bca', 'BolC1t03841H' => 'bol', 'BolC2t10992H' => 'bol', 'BolC6t38594H' => 'bol', 'BolC7t43693H' => 'bol', 'BraA01t03184Z' => 'bra', 'BraA02t08167Z' => 'bra', 'BraA06t27343Z' => 'bra', 'BraA07t31422Z' => 'bra', 'C01p38910' => 'bna', 'C02p48980' => 'bna', 'C06p34950' => 'bna', 'C06p46820' => 'bna', 'C07p31510' => 'bna', 'CAN.G1.64' => 'can', 'CAN.G1243.3' => 'can', 'CAN.G174.18' => 'can', 'CAN.G487.2' => 'can', 'CAN.G862.45' => 'can', 'CANSAT11G1457' => 'cansat', 'CANSAT56G0153' => 'cansat', 'CANSAT56G2986' => 'cansat', 'CARHR011200' => 'chi', 'CARHR011730' => 'chi', 'CARHR050660' => 'chi', 'CARHR065410' => 'chi', 'CARHR143620' => 'chi', 'CARHR247490' => 'chi', 'Carub.0001s1056' => 'cru', 'Carub.0002s0348' => 'cru', 'Carub.0002s1933' => 'cru', 'Carub.0005s0006' => 'cru', 'Ca_00088_v3' => 'car', 'Ca_05513_v3' => 'car', 'Ca_23114_v3' => 'car', 'Ca_23403_v3' => 'car', 'Ca_29927_v3' => 'car', 'CBR_g66668' => 'cbr', 'Cc02_g05290' => 'ccan', 'Cc02_g22300' => 'ccan', 'Cc04_g01110' => 'ccan', 'CDE05G3081' => 'cde', 'CDE05G3307' => 'cde', 'CDE05G3343' => 'cde', 'CDE06G0307' => 'cde', 'CDE06G1169' => 'cde', 'CDE06G2121' => 'cde', 'CDE06G2714' => 'cde', 'CDE07G0983' => 'cde', 'CDE10G1020' => 'cde', 'Cfa001204' => 'cfa', 'Cfa003515' => 'cfa', 'Cfa005543' => 'cfa', 'Cfa017023' => 'cfa', 'Ciclev10000891m.g' => 'ccl', 'Ciclev10011518m.g' => 'ccl', 'Ciclev10025379m.g' => 'ccl', 'Ciclev10031177m.g' => 'ccl', 'CiPaw.01G216500' => 'cil', 'CiPaw.06G148600' => 'cil', 'CiPaw.09G221900' => 'cil', 'ClCG07G005200' => 'cla', 'ClCG09G001110' => 'cla', 'ClCG10G022790' => 'cla', 'ClCG11G015480' => 'cla', 'COL.COLO4_08295' => 'col', 'COL.COLO4_10037' => 'col', 'COL.COLO4_17894' => 'col', 'COL.COLO4_30787' => 'col', 'Cpa.g.sc19.48' => 'cpa', 'Cpa.g.sc2.25' => 'cpa', 'Cpa.g.sc25.143' => 'cpa', 'Cpa.g.sc86.61' => 'cpa', 'CsaV3_4G028610' => 'csa', 'CsaV3_5G011050' => 'csa', 'CsaV3_7G034280' => 'csa', 'CSS0000744' => 'camsi', 'CSS0001533' => 'camsi', 'CSS0001770' => 'camsi', 'CSS0003409' => 'camsi', 'CSS0014521' => 'camsi', 'CSS0015486' => 'camsi', 'CSS0025836' => 'camsi', 'CSS0036266' => 'camsi', 'CSS0041189' => 'camsi', 'CSS0045574' => 'camsi', 'DCAR_005015' => 'dca', 'DCAR_007652' => 'dca', 'DCAR_023972' => 'dca', 'DCAR_027171' => 'dca', 'Dinv16972' => 'din', 'Dinv19353' => 'din', 'Dinv20413' => 'din', 'Dinv34493' => 'din', 'Dinv37850' => 'din', 'Duzib052G0469' => 'dzi', 'Duzib128G0022' => 'dzi', 'Duzib132G0308' => 'dzi', 'Duzib151G0461' => 'dzi', 'Duzib160G0257' => 'dzi', 'Duzib192G0357' => 'dzi', 'Duzib212G0307' => 'dzi', 'Duzib235G0938' => 'dzi', 'Duzib248G0979' => 'dzi', 'ECA233G4951' => 'eca', 'ECA234G4534' => 'eca', 'ECA247G2716' => 'eca', 'EL10Ac3g06114' => 'bvu', 'EL10Ac6g15371' => 'bvu', 'EL10Ac7g16438' => 'bvu', 'EL10Ac7g17109' => 'bvu', 'Eucgr.A00750' => 'egr', 'Eucgr.A00763' => 'egr', 'Eucgr.A00768' => 'egr', 'Eucgr.A00770' => 'egr', 'Eucgr.I02712' => 'egr', 'Eucgr.J00109' => 'egr', 'FAN01G2610' => 'fan', 'FAN02G0018' => 'fan', 'FAN02G0300' => 'fan', 'FAN03G0829' => 'fan', 'FAN04G3095' => 'fan', 'FAN05G4873' => 'fan', 'FAN05G5037' => 'fan', 'FAN05G5434' => 'fan', 'FAN06G2056' => 'fan', 'FAN08G2214' => 'fan', 'FAN09G0498' => 'fan', 'FAN09G3308' => 'fan', 'FAN10G2747' => 'fan', 'FAN13G1081' => 'fan', 'FAN14G1912' => 'fan', 'FAN14G4192' => 'fan', 'FAN18G2890' => 'fan', 'FvH4_5g30110' => 'fve', 'FvH4_6g09800' => 'fve', 'FvH4_6g35090' => 'fve', 'FvH4_7g26010' => 'fve', 'Glyma.07G041000' => 'gma', 'Glyma.07G107900' => 'gma', 'Glyma.08G184400' => 'gma', 'Glyma.11G160902' => 'gma', 'Glyma.11G161111' => 'gma', 'Glyma.15G048300' => 'gma', 'Glyma.16G009700' => 'gma', 'Glyma.16G130100' => 'gma', 'Gohir.A01G177100' => 'ghi', 'Gohir.A05G139300' => 'ghi', 'Gohir.A05G402400' => 'ghi', 'Gohir.A06G023532' => 'ghi', 'Gohir.A10G055700' => 'ghi', 'Gohir.A10G151400' => 'ghi', 'Gohir.A12G218850' => 'ghi', 'Gohir.A13G235700' => 'ghi', 'Gohir.D01G154950' => 'ghi', 'Gohir.D01G168000' => 'ghi', 'Gohir.D02G045750' => 'ghi', 'Gohir.D03G104666' => 'ghi', 'Gohir.D04G013033' => 'ghi', 'Gohir.D04G013100' => 'ghi', 'Gohir.D05G141500' => 'ghi', 'Gohir.D05G288101' => 'ghi', 'Gohir.D06G097750' => 'ghi', 'Gohir.D07G191850' => 'ghi', 'Gohir.D10G057600' => 'ghi', 'Gohir.D10G115000' => 'ghi', 'Gohir.D13G126332' => 'ghi', 'Gohir.D13G241400' => 'ghi', 'Gorai.002G208600' => 'gra', 'Gorai.003G068800' => 'gra', 'Gorai.008G028400' => 'gra', 'Gorai.009G145600' => 'gra', 'Gorai.011G061700' => 'gra', 'Gorai.011G126700' => 'gra', 'Gorai.012G015400' => 'gra', 'Gorai.013G074700' => 'gra', 'Gorai.013G272300' => 'gra', 'GSVIVG01011290001' => 'vvi', 'GSVIVG01016725001' => 'vvi', 'GSVIVG01023009001' => 'vvi', 'GSVIVG01030176001' => 'vvi', 'GSVIVG01032070001' => 'vvi', 'GSVIVG01032664001' => 'vvi', 'HanXRQChr04g0094371' => 'han', 'HanXRQChr04g0125281' => 'han', 'HanXRQChr08g0221581' => 'han', 'HanXRQChr10g0287411' => 'han', 'HanXRQChr10g0290411' => 'han', 'Haze_01629' => 'cav', 'Haze_16060' => 'cav', 'Haze_17363' => 'cav', 'Haze_21181' => 'cav', 'Hma1.2p1_0174F.1_g076790' => 'hma', 'Hma1.2p1_0217F.1_g091940' => 'hma', 'HPP92_002186' => 'vpl', 'HPP92_019115' => 'vpl', 'HPP92_024981' => 'vpl', 'Hund04331' => 'sun', 'Hund18678' => 'sun', 'Hund19759' => 'sun', 'Lalb_Chr04g0252651' => 'lal', 'Lalb_Chr04g0253691' => 'lal', 'Lalb_Chr10g0101381' => 'lal', 'Lalb_Chr12g0210651' => 'lal', 'Lalb_Chr17g0344701' => 'lal', 'Lalb_Chr18g0060831' => 'lal', 'Lj1A968T59' => 'lonja', 'Lj3C940T12' => 'lonja', 'Lj3g0007080' => 'lja', 'Lj3g0027692' => 'lja', 'Lj5A248G71' => 'lonja', 'Lj5C249T0' => 'lonja', 'Lj5C249T1' => 'lonja', 'Lj6g0013521' => 'lja', 'Lj8A53G90' => 'lonja', 'Lj9A308G29' => 'lonja', 'Lj9C534T4' => 'lonja', 'LjContig00408g0006549' => 'lja', 'Lsat_1_v5_gn_1_37881' => 'lsa', 'Lsat_1_v5_gn_5_109440' => 'lsa', 'Lsat_1_v5_gn_8_11421' => 'lsa', 'Lsat_1_v5_gn_9_38720' => 'lsa', 'Manes.04G147600' => 'mes', 'Manes.07G013900' => 'mes', 'Manes.08G170700' => 'mes', 'Manes.09G118500' => 'mes', 'Manes.10G001900' => 'mes', 'Manes.10G131800' => 'mes', 'Manes.11G017000' => 'mes', 'Mapoly0033s0030' => 'mpo', 'Mapoly0076s0018' => 'mpo', 'MBI03_g05801_MAGBIO' => 'mbi', 'MBI03_g11146_MAGBIO' => 'mbi', 'MBI13_g00699_MAGBIO' => 'mbi', 'MBI13_g47249_MAGBIO' => 'mbi', 'MBI19_g05292_MAGBIO' => 'mbi', 'MCO08G097' => 'mco', 'MD01G1168400' => 'mdo', 'MD07G1234400' => 'mdo', 'MD08G1225000' => 'mdo', 'MD09G1178800' => 'mdo', 'MD12G1189000' => 'mdo', 'MD15G1418500' => 'mdo', 'MD17G1164600' => 'mdo', 'Medtr2g007740' => 'mtr', 'Medtr5g067670' => 'mtr', 'Medtr8g005485' => 'mtr', 'Medtr8g005790' => 'mtr', 'Medtr8g021310' => 'mtr', 'MELO3C010436.2' => 'cme', 'MELO3C020159.2' => 'cme', 'MELO3C024337.2' => 'cme', 'Migut.D00929' => 'egut', 'Migut.F00576' => 'egut', 'Migut.I01101' => 'egut', 'Migut.N01035' => 'egut', 'MSTRG.164' => 'ama', 'MSTRG.22538' => 'ama', 'MSTRG.5237' => 'ama', 'MSTRG.8885' => 'ama', 'MSTRG.9528' => 'ama', 'Nitab4.5_0000078g0440' => 'nta', 'Nitab4.5_0000094g0080' => 'nta', 'Nitab4.5_0001215g0190' => 'nta', 'Nitab4.5_0004322g0040' => 'nta', 'Nitab4.5_0005153g0090' => 'nta', 'Nitab4.5_0006093g0030' => 'nta', 'Nitab4.5_0006232g0030' => 'nta', 'Nitab4.5_0006295g0010' => 'nta', 'Nitab4.5_0008052g0010' => 'nta', 'Nn5g26840' => 'nnu', 'Nn5g28070' => 'nnu', 'Nn6g35682' => 'nnu', 'Nn8g38589' => 'nnu', 'Oeu005581.1' => 'oeu', 'Oeu008878.1' => 'oeu', 'Oeu012745.1' => 'oeu', 'Oeu015499.1' => 'oeu', 'Oeu044919.1' => 'oeu', 'Oeu063992.2' => 'oeu', 'Os03g0334800' => 'osa', 'Os07g0614600' => 'osa', 'Os09g0439700' => 'osa', 'Os11g0546100' => 'osa', 'Peaxi162Scf00003g03826' => 'pax', 'Peaxi162Scf00038g01949' => 'pax', 'Peaxi162Scf00068g00074' => 'pax', 'Peaxi162Scf00304g00622' => 'pax', 'Peaxi162Scf01238g00008' => 'pax', 'Peaxi162Scf01238g00112' => 'pax', 'PGR031G0687' => 'pgr', 'PGR044G2504' => 'pgr', 'PGR102G0338' => 'pgr', 'PGR119G1661' => 'pgr', 'PGSC0003DMG400004366' => 'stu', 'PGSC0003DMG400017822' => 'stu', 'PGSC0003DMG400022887' => 'stu', 'PGSC0003DMG400027583' => 'stu', 'PGSC0003DMG400031223' => 'stu', 'Phvul.006G212300' => 'pvu', 'Phvul.010G057800' => 'pvu', 'Phvul.010G127700' => 'pvu', 'Potri.001G166500' => 'ptr', 'Potri.001G209400' => 'ptr', 'Potri.003G068500' => 'ptr', 'Potri.006G109000' => 'ptr', 'Potri.016G137700' => 'ptr', 'Pp3c1_24840' => 'ppa', 'Pp3c2_15830' => 'ppa', 'PRCOL_00000972' => 'pco', 'PRCOL_00001614' => 'pco', 'Prupe.1G562600' => 'ppe', 'Prupe.2G264800' => 'ppe', 'Prupe.3G038100' => 'ppe', 'Prupe.6G294600' => 'ppe', 'Psat0s115g0040' => 'psa', 'Psat1g106240' => 'psa', 'Psat1g219960' => 'psa', 'Psat2g063080' => 'psa', 'Psat4g167640' => 'psa', 'Psat4g209240' => 'psa', 'Psat5g157320' => 'psa', 'Psat7g042000' => 'psa', 'PSO017G7244' => 'pso', 'PSO063G0216' => 'pso', 'PSO170G5766' => 'pso', 'PSO386G0213' => 'pso', 'PSO421G0029' => 'pso', 'PSO724G0605' => 'pso', 'QL02p098604' => 'qlo', 'QL03p059914' => 'qlo', 'QL05p003857' => 'qlo', 'QL07p031979' => 'qlo', 'QL08p018255' => 'qlo', 'QL08p018257' => 'qlo', 'QL08p064916' => 'qlo', 'RcHm_v2.0_Chr1g0314071' => 'rch', 'RcHm_v2.0_Chr1g0372401' => 'rch', 'RcHm_v2.0_Chr1g0372411' => 'rch', 'RcHm_v2.0_Chr2g0146271' => 'rch', 'RcHm_v2.0_Chr3g0460391' => 'rch', 'RcHm_v2.0_Chr7g0224311' => 'rch', 'RcHm_v2.0_Chr7g0224371' => 'rch', 'Rhsim05G0231200' => 'rsi', 'Rhsim08G0240700' => 'rsi', 'Rhsim11G0131400' => 'rsi', 'Sabra01G0161700' => 'sbr', 'Sabra03G0040100' => 'sbr', 'Sabra04G0154000' => 'sbr', 'SalBow3G1029' => 'sbo', 'SalBow6G3427' => 'sbo', 'SalBow6G4751' => 'sbo', 'SalBow7G3527' => 'sbo', 'Sc12g0010740' => 'sci', 'Sc16g0003940' => 'sci', 'Sc20g0007020' => 'sci', 'Sed0000522' => 'sed', 'Sed0002616' => 'sed', 'Sed0014771' => 'sed', 'Sed0019574' => 'sed', 'Sed0019876' => 'sed', 'Sed0025951' => 'sed', 'SEGI_07850' => 'sgi', 'SEGI_19774' => 'sgi', 'SEGI_22709' => 'sgi', 'SEGI_30313' => 'sgi', 'SEGI_31665' => 'sgi', 'SEGI_38115' => 'sgi', 'SEGI_38181' => 'sgi', 'SGA_v2.0_scaffold145G36066' => 'sas', 'SGA_v2.0_scaffold305G47985' => 'sas', 'SGA_v2.0_scaffold44G16624' => 'sas', 'SGA_v2.0_scaffold4G02074' => 'sas', 'SGA_v2.0_scaffold60G20886' => 'sas', 'SGA_v2.0_scaffold68G22849' => 'sas', 'SHI16601' => 'shi', 'SHI25237' => 'shi', 'SHI25238' => 'shi', 'SMO116G0375' => 'smo', 'SMO117G0086' => 'smo', 'SMO364G0713' => 'smo', 'Solyc03g122250.3' => 'sly', 'Solyc06g048590.3' => 'sly', 'Solyc10g045600.2' => 'sly', 'Solyc10g074970.1' => 'sly', 'Solyc12g049390.2' => 'sly', 'Sopen03g040990' => 'spe', 'Sopen06g014780' => 'spe', 'Sopen10g015920' => 'spe', 'Sopen10g027460' => 'spe', 'Sopen12g023870' => 'spe', 'Sp2g12540' => 'spa', 'Sp5g27560' => 'spa', 'TAR381G1370' => 'tar', 'TAR623G0561' => 'tar', 'TAR624G0978' => 'tar', 'TAR629G1907' => 'tar', 'TAR633G2680' => 'tar', 'TAR636G1153' => 'tar', 'THA.LOC104808060' => 'tha', 'THA.LOC104812258' => 'tha', 'THA.LOC104823352' => 'tha', 'THA.LOC104823361' => 'tha', 'Thecc.02G041100' => 'tca', 'Thecc.04G150900' => 'tca', 'Thecc.06G123600' => 'tca', 'Thecc.10G177100' => 'tca', 'Thhalv10000865m.g' => 'esa', 'Thhalv10007387m.g' => 'esa', 'Thhalv10018416m.g' => 'esa', 'Thhalv10023415m.g' => 'esa', 'TPR.G16746' => 'tpr', 'TPR.G2068' => 'tpr', 'TPR.G27038' => 'tpr', 'TPR.G28725' => 'tpr', 'TWI34G0779' => 'twi', 'TWI53G0678' => 'twi', 'TWI59G1137' => 'twi', 'TWI63G1412' => 'twi', 'TWI73G0602' => 'twi', 'unitig_22.g5961' => 'ugi', 'unitig_578.g16606' => 'ugi', 'unitig_578.g16607' => 'ugi', 'unitig_88.g27821' => 'ugi', 'vmacro01775' => 'vma', 'vmacro15048' => 'vma', 'vmacro20373' => 'vma', 'VMungo0331G0727' => 'vmu', 'VMungo0331G1718' => 'vmu', 'VMungo0540G0359' => 'vmu', 'Zm00001eb015990' => 'zma', 'Zm00001eb032170' => 'zma', 'Zm00001eb032180' => 'zma', 'Zm00001eb032190' => 'zma', 'Zm00001eb100170' => 'zma', 'Zm00001eb103710' => 'zma', 'Zm00001eb113730' => 'zma', 'Zm00001eb314050' => 'zma', 'Zm00001eb395150' => 'zma' ) $gf_id = 'HOM05D001225' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001225' ) $data_identifier = 'HOM05D001225' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 6, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 9, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 6, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 22, 'gra' => (int) 9, 'vvi' => (int) 6, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 7, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 3, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395150' $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